It's covered. You're not the first person to have your dealer refuse to replace it. The folks that had problems with their dealers would either call the regional service rep or call corp isuzu up. Do either of the two and you will get it replaced for free.
http://www.isuzu.com/owners_warranty_2000to2002.jsp#
The thumping can be done by any old mechanic. I had my isuzu dealer do mine and they charged my 50 bucks.
The 2004 Rodeo's now have 1 peice drive shafts. I'm sure they are very pricey.
-Ryan